α,β-不饱和羰基化合物抗菌作用和机理的研究

采用全略微分重叠法对丁烯二酸及其酯类的量子化学参数进行了计算，并对该类化合物的分子结构特征与抗菌活性间的关系进行了相关分析．结果表明，丁烯二酸及其酯类抗菌活性依分子流水性能增强而提高，依分子内基团间作用力的增强而降低；随分子最低空轨道能量的降低，抗菌生物活性极显著上升（p＜0．01），抗代谢性能显著提高（p＜0．02）．α，β-不饱和羰基结构是该类化合物的抗菌功能域，其活性中心在β-碳和羰基氧。     

苯砜基环烷酸酯类化合物的分子结构与色谱保留的定量关系

根据线性溶解能理论，导出一种理论线性溶解相关模型，应用该模型及量子化学ＡＭＩ算法计算的分子结构参数，得出苯砜基环烷酸酯类化合物的分子结构与色谱保留定量关系方程，这个方程可以应用于同类化合物在同样色谱条件下保留行为的预测。研究表明，该类化合物的容量因子随着分子平均极化率的增大而增大，随着偶极矩和的分子中与硫原子相键合的氧原子的净电荷的增大而减小。     

拓扑量子方法及其在含C＝O和N＝O化合物性能估算中的应用

综合量子化学与拓扑化学知识, 提出了构建Y＝O (Y表示C, N)键拓扑量子键邻接矩阵的方法. 利用该矩阵特征根和量子化学原理, 计算了表征分子轨道能量、原子电荷和键级等的拓扑量子参数. 将这些参数对含C＝O, N＝O基团的有机分子的紫外吸收能量、红外伸缩振动频率和醛酮C＝O上的亲核加成反应速率等性质进行定量结构-性质相关, 得到的模型均具有良好的估算能力.     

π-σ轨道作用能分解法和限制万轨道作用的几何优化

简要地介绍能量分解法的发展历史，强调能量分解的特点是给量子化学的计算提供明确的化学意义，介绍本实验室建立的能量分解法和限制轨道作用的几何优化法。在这两个方法的基础上，论证了丌．电子离域是失稳定的；颠倒了经典有机结构理论中基本的因果关系——共轭效应和构象之间的因果关系；为芳香能的计算提供了一个新的模型和新的方法，表明芳香能的计算不再需要参考分子；定量地区别静电作用和电子离域在化学键形成中的作用；定量地讨论取代基效应和张力芳环的扭曲驱动力。     

原子团族P6同分异构体的可能性

使用分子图形学方法设计出２３种可能的同分异构体，并对共进行了分子力学、ＰＭ３半经验量子化学和ＡＤＦ密度泛函优化。在Ｐ６原子团簇模型设计中，磷原子采用一、二、三或四配位。从各异构体的比较可得知，由正四面体Ｐ４派生出的结构在能量方面具有优势。椅式结构，船式结构和平面结构的能量依次增大。     

C2D2和C2H2分子键-键耦合研究

采用Morse根于描述C_2D_2分子中C－D键的伸缩振动，用谐振子描述C－C键伸缩振动，更新构造了C2D2分子的振动哈密顿，自行设计了非线性最小二乘拟合程序，并用它对C2D2分子的伸缩振动能级进行拟合，得到了基本的势能参数．理论计算与实验结果符合得很好，拟会的标准差为1.14cm－1；利用这些参数进一步计算了C2H2和C2D2的振动能级．     

碱金属与碱土金属卤化物电荷分布和偶极矩的ABEEMσπ模拟

应用原子键电负性均衡方法模型(ABEEMσπ模型),通过大量量子化学计算,拟合确定了含碱金属和碱土金属的卤化物体系的ABEEMσπ参数.ABEEMσπ模型计算得到的电荷分布与从头算计算的电荷分布有很好的一致性.同时计算了模型分子的偶极矩,与实验值具有很好的一致性.研究表明ABEEMσπ模型可以很好地应用于含碱金属和碱土金属的卤化物的结构和性质的分析.     

取代吡唑类化合物对肿瘤抑制活性的QSAR研究与分子设计

采用量子化学中的密度泛函理论(DFT)方法,在B3LYP/6-31++G(d,p)基组水平上系统计算了TβR-I抑制剂吡唑类衍生物(AHSPs)的量子化学结构参数。用逐步线性回归方法(SR)对该类AHSPs化合物进行了定量构效关系研究,筛选出了影响化合物抑制活性的主要因素,得到了最优QSAR方程。研究结果表明,抑制剂分子的偶极矩μ、疏水系数logP、分子中吡啶环的7-N原子的Mulliken电荷是影响AHSPs类化合物的抑制活性的主要因素。偶极矩μ和疏水系数logP越小,吡啶环的7-N原子Mulliken净电荷越正,则化合物的抑制活性越强。所得模型对该类吡唑类化合物针对TβR-Ⅰ的抑制活性有较好的预测结果,据此设计出14个新型AHSPs分子,计算其量子力学参数,利用构效方程预测出新型AHSPs分子的性能,发现其中有3个分子可能有较好的理论抑制活性。     

醇类化合物热值改进剂的定量结构-性质关系研究

醇类化合物燃料作为一种新型的可再生清洁能源,目前是代替燃油及煤的优良环保型燃料.本文计算表征了醇类化合物热值改进剂的4个分子连接性指数和5个量子化学参数,用多元线性回归方法对参数进行了优化筛选,获得了醇类化合物热值改进剂的定量结构与热值性质的关系模型,其相关系数R为0.961.计算结果表明:与醇类化合物热值改进剂的热值显著相关的变量是最低空轨道能量ELUMO、最低空轨道能量与最高占有轨道能量差△E、总能量ET,预测值与相应的实验值较好吻合,所建模型具有良好稳定性和预测能力,与分子连接性指数等的相关程度较好.     

α，β－不饱和羰基化合物的分子结构特性与抗菌活性间的关系

采用全略微分重叠法计算了丁烯二酸及其酯类的量子化学参数，并对该类化合物的分子结构特征与抗菌活性间的关系进行了相关分析，结果表明，丁烯二酸及其酯类抗菌活性依分子疏水性能增强而提高，依分子内基团间作用力的增强而减小，随分子最低空轨道能量的降低，抗菌生物活性极显著上升（ρ＜０．０１），抗代谢性能显著增加（ρ＜０．０２）。α，β－不饱和羰基结构是该类化合物的抗菌功能域，其活性中心在β－碳和羰基氧。     

磺酰胺类常咯啉的分子力学参数的确定

应用量子化学ＭＮＤＯ程序及分子力学ＭＭＰ２程序，确定了一些未知磺酰胺类常咯啉的分子力学参数。应用这些参数计算了几个晶体结构已知的磺酰胺类化合物，与真实结构比较，计算结果令人满意。由此说明确定的分子力学参数用于计算磺酰胺类化合物时的正确性和可行性。     

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.     

Influence of the Temperature on the Crystal Structure of Poly(p‐phenylene sulfide): A Study by X‐Ray Measurements and Molecular Mechanics

The crystal structure of poly(p‐phenylene sulfide) (PPS) has been investigated by X‐ray analysis on fiber samples and by molecular mechanics calculations over a wide range of temperatures, from 0 K to 548 K, showing that all the structural parameters remain substantially constant. The thermal expansion coefficients of the a and b axes have been evaluated. Structural parameters experimentally obtained at the various temperatures have been used in calculations by molecular mechanics. The crystal structures calculated by various methods and using several potential functions are in very good agreement. New parameters are proposed for the nonbonded terms of the potential functions.     

Molecular mechanics force-field parameterization procedures

A set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve-fitting program to generate force field parameters from raw data is given in Appendix I.     

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

We describe the development of the AMBER force field parameters for 46 nucleases involving most kinds of copper nucleases with high DNA affinities and specificities by MINA approach that could evaluate accurate force constants for batch bonds/angles on the basis of energies of three adjacent lengths/angles geometries. The molecular mechanics (MM) and molecular dynamic simulations on adducts of the 21 representative copper-based nucleases with DNA are in excellent agreement with those of experimental results. Furthermore, to validate the evaluated parameters, the studied structures performed frequency analysis together with normal mode calculations in quantum mechanics and MM calculations. The force field parameters evaluated in this work provide an extension of AMBER force field, and the results of molecular dynamics simulations of adduct of copper nuclease and duplex DNA illustrate the potential utility of these parameters.     

Fractal phenomena in molecular mechanics calculation

It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation.     

Force field parameters for the simulation of modified histone tails

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Simulations of X-ray absorption spectra: the effect of the solvent

We perform quantum mechanics/molecular mechanics molecular dynamics simulations on the [Pt(2)(P(2)O(5)H(2))(4)](4-) (abbreviated PtPOP) complex; in water, dimethylformamide and ethanol. These are used to calculate the ground state X-ray absorption spectrum of the complex. The structural parameters from X-ray spectra are usually extracted using a fit of the experimental data. In such simulations the solvent is neglected meaning that any effect of the local environment will be compensated for by structural changes of the solute, leading to possible discrepancies in the extracted structural parameters. Our simulations show a significant solvent effect on the spectra, which has important implications for the structural analysis of molecules in solution.     

Impact testing of plastics: Present knowledge

This work takes a look at the present knowledge of the impact resistance of plastics. Two approaches are discussed and examined: the first is instrumented impact testing, and the second is that proposed by Williams and coworkers at Imperial College, London. The advantages of both are discussed and examined with particular reference to fracture mechanics analysis of impact data. It is shown that fracture mechanics gives a satisfactory theoretical assessment of the whole problem and many of the most important parameters of the material can now be determined by impact testing.     

硝酸酯类分子力学参数的确定和应用

运用MM2(85年版)分子力学程序, 以硝酸甲酯、硝酸乙酯的实验结构为参比, 调试确定了硝酸酯类化合物的伸缩力常数(K~s)、弯曲力常数(K~b)和旋转力常数(V~1、V~2、和V~3)。用这套力场参数计算了硝酸甲酯、硝酸乙酯和硝化甘油的平衡几何构型、生成热和偶极矩, 计算结果与实验值和从头计算结果相一致。还用这套参数计算了结构未见报道的异基硝酸酯、丙烯基硝酸酯和苯基硝酸酯, 所得结果与MNDO全优化几何构型相符。